Next-Generation Sequencing Yields the Complete Mitochondrial Genome of the Longfang Moray, Enchelynassa Canina (Anguilliformes: Muraenidae)

http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic)

Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1030629

MITOGENOME ANNOUNCEMENT Next-generation sequencing yields the complete mitochondrial genome of the longfang moray, Enchelynassa canina (Anguilliformes: Muraenidae)

Kar-Hoe Loh1, Kwang-Tsao Shao2, Hong-Ming Chen3, Ching-Hung Chen4, Poh-Leong Loo1, Amy Then Yee Hui5, Phaik-Eem Lim1, Ving-Ching Chong1, Kang-Ning Shen6, and Chung-Der Hsiao7

1Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia, 2Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, 3Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan, 4WeThink Biotech INC., Taoyuan, Taiwan, 5Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia, 6Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan, and 7Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan

Abstract Keywords In this study, the complete mitogenome sequence of the longfang moray, Enchelynassa canina Longfang moray, mitogenome, (Anguilliformes: Muraenidae) has been sequenced by the next-generation sequencing method. next-generation sequencing The length of the assembled mitogenome is 16,592 bp, which includes 13 protein coding genes, 22 transfer RNAs, and 2 ribosomal RNAs genes. The overall base composition of History longfang moray is 28.4% for A, 28.0% for C, 18.4% for G, 25.1% for T, and show 82% identities to Kidako moray, Gymnothorax kidako. The complete mitogenome of the longfang moray Received 6 March 2015 provides an essential and important DNA molecular data for further phylogeography and Revised 9 March 2015 evolutionary analysis for moray eel phylogeny. Accepted 14 March 2015 Published online 27 May 2015

For personal use only. Longfang moray, Enchelynassa canina is a special species with The complete mitochondrial genome of E. canina was 16,592 bp anterior nostril bears a bilobate fleshy large projectting tube, in size (GenBank: KP893074), includes 13 protein coding genes, posterior nostril in front of and above the eye, surrounded by a 22 transfer RNAs, and two ribosomal RNAs genes. The overall fleshy rim. Body color is uniform brownish, and grey color in the base composition of E. canina is 28.4% for A, 28.0% for C, 18.4% belly side. It is a type species (synonyms E. bleekeri) and the only for G, 25.1% for T, and show 82% identities to Kidako moray, member of the genus Enchelynassa. This species is widely Gymnothorax kidako. distributed in Indo-Pacific: Chagos Island and Reunion, to The protein coding, rRNA, and tRNA genes of E. canina Panama, north to Japan and the Hawaiian Islands, Taiwan, north mitogenome were predicted by using DOGMA (Wyman et al., to China, south to Tonga and Mangareva. Adults live in reef flats 2004), ARWEN (Laslett & Canback, 2008), and MitoAnnotator and inhabits areas with strong surge in a depth of 2–20 m. This (Iwasaki et al., 2013) tools. All protein-coding genes were species is very secretive during the day, feeds on fishes and encoded on the H-strand with exception of protein-coding genes

Mitochondrial DNA Downloaded from informahealthcare.com by Academia Sinica on 06/29/15 octopus at night. Jaw elongate and arched, elongate canine teeth of ND6. All tRNA genes were encoded on the H-strand with the exposed when mouth closed, it may traumatogenis to humans exception of tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA- when provoked. The establishment of longfang moray mitogen- Tyr, tRNA-Ser (UGA) tRNA-Glu, and tRNA-Pro genes. All the 13 ome is useful for further phylogenetic research studies. mitochondrial protein-coding genes share the start codon ATG, Samples (voucher no. 350) of E. canina were collected from except for COX1 (GTG start codon). It also important to note that Changbin, Taiwan. The methods for genomic DNA extraction, four of the 13 protein-coding genes is inferred to terminate with library construction, and next-generation sequencing were TAA termination codon (ND1, ATP8, ND4L, and CYTB), 2 followed by our previous publication (Shen et al., 2014). The terminated with TAG codon (ND5 and ND6), 7 of them are raw next-generation sequencing reads generated from MiSeq terminated with incomplete codons of T– (ND2, CO1, CO2, ND3, (Illumina, San Diego, CA) were de novo assembled by and ND4) or TA– (ATP6 and CO3). Many fishes also used such commercial software (Geneious V8, Auckland, New Zealand) to incomplete codon structure as a signal to halt the process of produce a single, circular form of complete mitogenome with protein translation. The longest one is ND5 gene (1842 bp) in all about an average 28 Â coverage (1390 out of 5,539,274, 0.03%). protein coding genes, whereas the shortest is ATP8 gene (168 bp). The two ribosomal RNA genes, 12S rRNA gene (949 bp) and 16S rRNA gene (1664 bp), are located between tRNA-Phe and tRNA- Corresponding: Kang-Ning Shen, Center of Excellence for the Oceans, Leu (UAA) and separated by tRNA-Val. The length of D-loop National Taiwan Ocean University, Keelung 20224, Taiwan. E-mail: control region is 938 bp. [email protected] Chung-Der Hsiao, Department of Bioscience Technology, Chung Yuan To validate the phylogenetic position of E. canina, we have Christian University, Chung-Li 32023, Taiwan. E-mail: cdhsiao@ constructed a maximum likelihood phylogenetic tree (with 500 cycu.edu.tw bootstrap replicates) by using the complete mitogenome of 2 K.-H. Loh et al. Mitochondrial DNA, Early Online: 1–2

Figure 1. Molecular phylogeny of Enchelynassa canina and other related species in Anguilliformes based on complete mitogenome. The complete mitogenomes is downloaded from GenBank and the phylogenic tree is constructed by the maximum likelihood method with 500 bootstrap replicates. The gene’s accession number for tree construction is listed as follows: Coloconger cadenati (NC_013606), Derichthys serpentinus (NC_013611), Facciolella oxyrhyncha (NC_013621), Ilyophis brunneus (NC_013634), Myrichthys maculosus (NC_013635), Cynoponticus ferox (NC_013617), Avocettina infans (NC_013624), Serrivomer beanii (NC_013627), Anguilla japonica (NC_002707), Moringua edwardsi (NC_013622), Kaupichthys hyoproroides (NC_013607), Ariosoma shiroanago (NC_013632), Cyema atrum (NC_013609), Monognathus jesperseni (NC_013612), Eurypharynx pelecanoides (NC_005299), Saccopharynx lavenbergi (NC_005298), Pythonichthys microphthalmus (NC_013601), Myroconger compressus (NC_013631), Scuticaria tigrina (KP874183), Anarchias sp. Ansp (NC_013613), Gymnomuraena zebra (KP793920), Rhinomuraena quaesita For personal use only. (NC_013610), Enchelynassa canina (KP893074), Gymnothorax kidako (NC_004417), Notacanthus chemnitzi (NC_005144) and Elops hawaiensis (NC_005798).

24 species derived from 19 different families in order References Anguilliformes. By following the analysis method described in Inoue JG, Miya M, Miller MJ, Sado T, Hanel R, Hatooka K, Aoyama J, the previous publication (Inoue et al., 2010), Notacanthus et al. (2010). Deep-ocean origin of the freshwater eels. Biol Lett chemnitzi and Elops hawaiensis, which produce leptocephalus 6:363–6. larvae, were used as an outgroup for tree rooting. Result shows that Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, E. canina can be unambiguously grouped in Muraenidae which is Sado T, et al. (2013). MitoFish and MitoAnnotator: A mitochondrial Mitochondrial DNA Downloaded from informahealthcare.com by Academia Sinica on 06/29/15 closely related to Gymnothorax kidako with high-bootstrap value genome database of fish with an accurate and automatic annotation supported (Figure 1). In conclusion, the complete mitogenome of pipeline. Mol Biol Evol 30:2531–40. Laslett D, Canback B. (2008). ARWEN: A program to detect tRNA E. canina the deduced in this study provides an essential and genes in metazoan mitochondrial nucleotide sequences. Bioinformatics important DNA molecular data for further phylogeography and 24:172–5. evolutionary analysis for moray eel phylogeny. Shen KN, Yen TC, Chen CH, Li HY, Chen PL, Hsiao CD. (2014). Next generation sequencing yields the complete mitochondrial genome of Declaration of interest the flathead mullet, Mugil cephalus cryptic species NWP2 (Teleostei: Mugilidae). Mitochondrial DNA 26:1–2. The authors report that they have no conflicts of interest. The authors Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of alone are responsible for the content and writing of the paper. organellar genomes with DOGMA. Bioinformatics 20:3252–5.